Darryl Nelson | The University of Sydney (original) (raw)

Papers by Darryl Nelson

Soil Biology & Biochemistry, 1998

An aerobic, Gram-positive bacterium was isolated from explosives-contaminated soil by enrichment ... more An aerobic, Gram-positive bacterium was isolated from explosives-contaminated soil by enrichment culture, using the nitramine explosive, hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX), as the sole added N source. The organism, identified by 16S rDNA analysis as a Rhodococcus sp., strain DN22, grew exponentially with a mean generation time of 6.5 h at 25°C in minimal medium containing RDX as the sole N source. The growth medium was depleted of RDX 24 h after inoculation but growth did not cease until 20 h later. It was concluded that strain DN22 was using NO−2, released from RDX, as a growth substrate because, following inoculation of strain DN22 into RDX-containing minimal medium, the concentration of NO−2 increased during the first 10 h of incubation and declined to undetectable amounts 20 h later. The ratio of the growth yields of strain DN22 grown on RDX or NO−3 as N sources indicated that three of the six N atoms of RDX were being incorporated into biomass. Increased concentrations of NH+4 in the growth medium reduced the extent of RDX degradation. Nitrite was produced from RDX by resting cell suspensions grown on RDX, NO−3, NO−2 or glutamine as N sources, but not by cells grown on NH+4–N or in peptone-yeast extract medium. Resting cells grown on RDX showed the highest degradative activity, compared to cells grown on alternative N sources, indicating that the RDX degradation system is inducible. When soil was inoculated with RDX-grown cells of strain DN22rr, a rifampicin-resistant derivative of strain DN22, there was significant biodegradation of RDX. The addition of oat chaff to soil stimulated the growth of strain DN22rr and enhanced biodegradation of RDX, resulting in 90% degradation of the explosive in 21 d.

Antonie Van Leeuwenhoek International Journal of General and Molecular Microbiology, 2008

Most bacteria possess the enzyme acetohydroxyacid synthase, which is used to produce branched-cha... more Most bacteria possess the enzyme acetohydroxyacid synthase, which is used to produce branched-chain amino acids. Enteric bacteria contain several isozymes suited to different conditions, but the distribution of acetohydroxyacid synthase in soil bacteria is largely unknown. Growth experiments confirmed that Escherichia coli, Salmonella enterica serotype Typhimurium, and Enterobacter aerogenes contain isozymes of acetohydroxyacid synthase, allowing the bacteria to grow in the presence of valine (which causes feedback inhibition of AHAS I) or the sulfonylurea herbicide triasulfuron (which inhibits AHAS II) although a slight lag phase was observed in growth in the latter case. Several common soil isolates were inhibited by triasulfuron, but Pseudomonas fluorescens and Rhodococcus erythropolis were not inhibited by any combination of triasulfuron and valine. The extent of sulfonylurea-sensitive acetohydroxyacid synthase in soil was revealed when 21 out of 27 isolated bacteria in pure culture were inhibited by triasulfuron, the addition of isoleucine and/or valine reversing the effect in 19 cases. Primers were designed to target the genes encoding the large subunits (ilvB, ilvG and ilvI) of acetohydroxyacid synthase from available sequence data and a ∼355 bp fragment in Bacillus subtilis, Arthrobacter globiformis, E. coli and S. enterica was subsequently amplified. The primers were used to create a small clone library of sequences from an agricultural soil. Phylogenetic analysis revealed significant sequence variation, but all 19 amino acid sequences were most closely related to published large subunit acetohydroxyacid synthase amino acid sequences within several phyla including the Proteobacteria and Actinobacteria. The results suggested the majority of soil microorganisms contain only one functional acetohydroxyacid synthase enzyme sensitive to sulfonylurea herbicides.

Soil Biology & Biochemistry, 2007

Two of the major constraints to grain production in large areas of South-East Australia and cropp... more Two of the major constraints to grain production in large areas of South-East Australia and cropping soils worldwide are high levels of subsoil boron (B) and excessive salinity (NaCl). Although the effect of these constraints is often studied in plants, the effect on microbially mediated plant-beneficial processes is unclear. To that end, we investigated the impact of B and NaCl on soil microbial community structure (MCS) in the wheat rhizosphere using BIOLOG ecoplates and terminal restriction fragment length polymorphism (T-RFLP). In addition, the effects of B and NaCl on the nitrogen (N) cycle processes of N fixation and ammonia oxidation were assessed by the construction of clone libraries of diazotrophic (nifH) and ammonia oxidising (amoA) rhizobacteria. Analysis of BIOLOG plates using non-metric multidimensional scaling (MDS) revealed addition of both B and NaCl significantly changed MCS, the latter of which was also significant through the analysis of T-RFLP data. Utilisation of several chemical groups of BIOLOG substrates significantly changed in NaCl-amended soil; both B and NaCl affected utilisation of several individual substrates indicative of plant stress including serine and malic acid. A significant decrease in diversity and species richness was observed in high B rhizosphere soil. The community structure of ammonia-oxidising bacteria (AOB), all of which clustered with Nitrosospira-like sequences, did not significantly change in response to addition of B or NaCl, but addition of the latter resulted in a significant increase of diazotroph clones within the α-proteobacteria similar to Azospirillum sp. It appeared that the addition of B and NaCl to soil changed rhizosphere MCS indirectly through increased soil moisture and subtle changes in root exudate patterns, the addition of the latter producing a more distinct change through increased osmotic pressure, leading to a greater increase in rhizodeposition of nutrients, especially carbohydrates. The implications for the current study are that B and NaCl are more likely to affect rhizosphere MCS indirectly through root exudate quantity and/or quality than directly through microbial toxicity, and that plant health is a major determinant in rhizosphere MCS and normal N cycling.

Australian Journal of Soil Research, 2006

... by vacuum centrifugation (50 ◦ C, 30 min). Samples were analysed using an ABI Prism 3700 plat... more ... by vacuum centrifugation (50 ◦ C, 30 min). Samples were analysed using an ABI Prism 3700 platform with Genotyper 2.1 software (Australian Genomic Research Facility, Australia). Cloning and sequencing of nifH PCR amplicons ...

Isme Journal, 2007

The role of environmental selection in governing the structure of communities of freshwater sulfu... more The role of environmental selection in governing the structure of communities of freshwater sulfur bacteria (Achromatium spp) was experimentally tested by mixing sediments from two geographically separated lakes (Rydal Water (RY) and Hell Kettles (HK)) that harboured Achromatium spp. Community profiles of Achromatium spp in sediment microcosms at day 0 and after 60 days were compared to determine whether initial Achromatium community composition or subsequent selection by the sediment environment had greater influence in dictating the final Achromatium community structure. It was found that Achromatium spp from the HK community became established in mixed sediments at the expense of members of the RY community. This selection for the HK Achromatium community was more pronounced when sediment composition was manipulated to resemble HK sediments. Our findings definitively demonstrate that environmental selection is the primary determinant of Achromatium community structure in these sediments.

Soil Biology & Biochemistry, 1998

An aerobic, Gram-positive bacterium was isolated from explosives-contaminated soil by enrichment ... more An aerobic, Gram-positive bacterium was isolated from explosives-contaminated soil by enrichment culture, using the nitramine explosive, hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX), as the sole added N source. The organism, identified by 16S rDNA analysis as a Rhodococcus sp., strain DN22, grew exponentially with a mean generation time of 6.5 h at 25°C in minimal medium containing RDX as the sole N source. The growth medium was depleted of RDX 24 h after inoculation but growth did not cease until 20 h later. It was concluded that strain DN22 was using NO−2, released from RDX, as a growth substrate because, following inoculation of strain DN22 into RDX-containing minimal medium, the concentration of NO−2 increased during the first 10 h of incubation and declined to undetectable amounts 20 h later. The ratio of the growth yields of strain DN22 grown on RDX or NO−3 as N sources indicated that three of the six N atoms of RDX were being incorporated into biomass. Increased concentrations of NH+4 in the growth medium reduced the extent of RDX degradation. Nitrite was produced from RDX by resting cell suspensions grown on RDX, NO−3, NO−2 or glutamine as N sources, but not by cells grown on NH+4–N or in peptone-yeast extract medium. Resting cells grown on RDX showed the highest degradative activity, compared to cells grown on alternative N sources, indicating that the RDX degradation system is inducible. When soil was inoculated with RDX-grown cells of strain DN22rr, a rifampicin-resistant derivative of strain DN22, there was significant biodegradation of RDX. The addition of oat chaff to soil stimulated the growth of strain DN22rr and enhanced biodegradation of RDX, resulting in 90% degradation of the explosive in 21 d.

Antonie Van Leeuwenhoek International Journal of General and Molecular Microbiology, 2008

Most bacteria possess the enzyme acetohydroxyacid synthase, which is used to produce branched-cha... more Most bacteria possess the enzyme acetohydroxyacid synthase, which is used to produce branched-chain amino acids. Enteric bacteria contain several isozymes suited to different conditions, but the distribution of acetohydroxyacid synthase in soil bacteria is largely unknown. Growth experiments confirmed that Escherichia coli, Salmonella enterica serotype Typhimurium, and Enterobacter aerogenes contain isozymes of acetohydroxyacid synthase, allowing the bacteria to grow in the presence of valine (which causes feedback inhibition of AHAS I) or the sulfonylurea herbicide triasulfuron (which inhibits AHAS II) although a slight lag phase was observed in growth in the latter case. Several common soil isolates were inhibited by triasulfuron, but Pseudomonas fluorescens and Rhodococcus erythropolis were not inhibited by any combination of triasulfuron and valine. The extent of sulfonylurea-sensitive acetohydroxyacid synthase in soil was revealed when 21 out of 27 isolated bacteria in pure culture were inhibited by triasulfuron, the addition of isoleucine and/or valine reversing the effect in 19 cases. Primers were designed to target the genes encoding the large subunits (ilvB, ilvG and ilvI) of acetohydroxyacid synthase from available sequence data and a ∼355 bp fragment in Bacillus subtilis, Arthrobacter globiformis, E. coli and S. enterica was subsequently amplified. The primers were used to create a small clone library of sequences from an agricultural soil. Phylogenetic analysis revealed significant sequence variation, but all 19 amino acid sequences were most closely related to published large subunit acetohydroxyacid synthase amino acid sequences within several phyla including the Proteobacteria and Actinobacteria. The results suggested the majority of soil microorganisms contain only one functional acetohydroxyacid synthase enzyme sensitive to sulfonylurea herbicides.

Soil Biology & Biochemistry, 2007

Two of the major constraints to grain production in large areas of South-East Australia and cropp... more Two of the major constraints to grain production in large areas of South-East Australia and cropping soils worldwide are high levels of subsoil boron (B) and excessive salinity (NaCl). Although the effect of these constraints is often studied in plants, the effect on microbially mediated plant-beneficial processes is unclear. To that end, we investigated the impact of B and NaCl on soil microbial community structure (MCS) in the wheat rhizosphere using BIOLOG ecoplates and terminal restriction fragment length polymorphism (T-RFLP). In addition, the effects of B and NaCl on the nitrogen (N) cycle processes of N fixation and ammonia oxidation were assessed by the construction of clone libraries of diazotrophic (nifH) and ammonia oxidising (amoA) rhizobacteria. Analysis of BIOLOG plates using non-metric multidimensional scaling (MDS) revealed addition of both B and NaCl significantly changed MCS, the latter of which was also significant through the analysis of T-RFLP data. Utilisation of several chemical groups of BIOLOG substrates significantly changed in NaCl-amended soil; both B and NaCl affected utilisation of several individual substrates indicative of plant stress including serine and malic acid. A significant decrease in diversity and species richness was observed in high B rhizosphere soil. The community structure of ammonia-oxidising bacteria (AOB), all of which clustered with Nitrosospira-like sequences, did not significantly change in response to addition of B or NaCl, but addition of the latter resulted in a significant increase of diazotroph clones within the α-proteobacteria similar to Azospirillum sp. It appeared that the addition of B and NaCl to soil changed rhizosphere MCS indirectly through increased soil moisture and subtle changes in root exudate patterns, the addition of the latter producing a more distinct change through increased osmotic pressure, leading to a greater increase in rhizodeposition of nutrients, especially carbohydrates. The implications for the current study are that B and NaCl are more likely to affect rhizosphere MCS indirectly through root exudate quantity and/or quality than directly through microbial toxicity, and that plant health is a major determinant in rhizosphere MCS and normal N cycling.

Australian Journal of Soil Research, 2006

... by vacuum centrifugation (50 ◦ C, 30 min). Samples were analysed using an ABI Prism 3700 plat... more ... by vacuum centrifugation (50 ◦ C, 30 min). Samples were analysed using an ABI Prism 3700 platform with Genotyper 2.1 software (Australian Genomic Research Facility, Australia). Cloning and sequencing of nifH PCR amplicons ...

Isme Journal, 2007

The role of environmental selection in governing the structure of communities of freshwater sulfu... more The role of environmental selection in governing the structure of communities of freshwater sulfur bacteria (Achromatium spp) was experimentally tested by mixing sediments from two geographically separated lakes (Rydal Water (RY) and Hell Kettles (HK)) that harboured Achromatium spp. Community profiles of Achromatium spp in sediment microcosms at day 0 and after 60 days were compared to determine whether initial Achromatium community composition or subsequent selection by the sediment environment had greater influence in dictating the final Achromatium community structure. It was found that Achromatium spp from the HK community became established in mixed sediments at the expense of members of the RY community. This selection for the HK Achromatium community was more pronounced when sediment composition was manipulated to resemble HK sediments. Our findings definitively demonstrate that environmental selection is the primary determinant of Achromatium community structure in these sediments.